to.genee: to.genee

In GENE.E: Interact with GENE-E from R

Description

R interface to view a matrix in GENE-E

Usage

to.genee(mdat, row.annotations=NULL, column.annotations=NULL, show.rownames=T, show.colnames=T, row.hclust=NULL, column.hclust=NULL, url='http://localhost:9998')

Arguments

mdat	a matrix.
row.annotations	a data frame containing row annotations.
column.annotations	a data frame containing column annotations.
show.rownames	Whether to show the row names of the matrix in GENE-E.
show.colnames	Whether to show the column names of the matrix in GENE-E.
row.hclust	An object of class hclust to show in GENE-E. If provided, the matrix and annotations will be reordered to reflect the tree produced by the clustering process.
column.hclust	An object of class hclust to show in GENE-E. If provided, the matrix and annotations will be reordered to reflect the tree produced by the clustering process.
url	GENE-E URL.

Details

R interface to GENE-E.

Examples

# not run
# z = matrix(rnorm(30),nrow=5,ncol=6);
# row.names(z) <- LETTERS[1:NROW(z)];
# colnames(z) <- LETTERS[1:NCOL(z)];
# row.annotations <- data.frame(y=1:5, char = I(letters[1:5]))
# L3 <- LETTERS[1:3]  
# column.annotations <- data.frame(y=1:6, char = I(letters[1:6]), fac=sample(L3, 6, replace=TRUE))
# to.genee(z, row.annotations, column.annotations, column.hclust=hclust(dist(t(z))));

Example output

Loading required package: rhdf5
Loading required package: RCurl
Loading required package: bitops

GENE.E documentation built on May 31, 2017, 3:11 p.m.